Here is a list of all documented files with brief descriptions:

_context.cpp
_context.h
aera_hand_robot_controller.cpp
AERA_main.cpp
ast_controller.cpp
ast_controller.h
ast_controller.tpl.cpp
atom.cpp
atom.h
atom.inline.cpp
auto_focus.cpp
auto_focus.h
auto_focus_callback.cpp
auto_focus_callback.h
base.cpp
base.h
base.tpl.cpp
binding_map.cpp
binding_map.h
r_exec/callbacks.cpp
usr_operators/Callbacks/callbacks.cpp
r_exec/callbacks.h
usr_operators/Callbacks/callbacks.h
class.cpp
class.h
code_utils.cpp
compiler.cpp
compiler.h
context.cpp
context.h
controller.h
cpp_programs.cpp
cpp_programs.h
cst_controller.cpp
cst_controller.h
decompiler.cpp
decompiler.h
dll.h
factory.cpp
factory.h
g_monitor.cpp
g_monitor.h
group.cpp
group.h
group.inline.cpp
guard_builder.cpp
guard_builder.h
hlp_context.cpp
hlp_context.h
hlp_controller.cpp
hlp_controller.h
hlp_overlay.cpp
hlp_overlay.h
image.cpp
image.h
image.tpl.cpp
image_impl.cpp
image_impl.h
init.cpp
init.h
list.h
AERA/main.cpp
output_window/main.cpp
main.h
mdl_controller.cpp
mdl_controller.h
mem.cpp
mem.h
mem.tpl.cpp
mem_output.h
model_base.cpp
model_base.h
monitor.cpp
monitor.h
object.cpp
r_code/object.h
r_exec/object.h
object.tpl.cpp
opcodes.cpp
opcodes.h
operator.cpp
operator.h
operators.cpp
operators.h
out_stream.h
overlay.cpp
overlay.h
p_monitor.cpp
p_monitor.h
pattern_extractor.cpp
pattern_extractor.h
pgm_controller.cpp
pgm_controller.h
pgm_overlay.cpp
pgm_overlay.h
pgm_overlay.inline.cpp
pipe.h
pipe.tpl.cpp
preprocessor.cpp
preprocessor.h
r_code.cpp
r_code.h
r_comp.cpp
r_comp.h
reduction_core.cpp
reduction_core.h
reduction_job.cpp
reduction_job.h
replicode_defs.h
resized_vector.h
segments.cpp
segments.h
settings.h
structure_member.cpp
structure_member.h
tcp_connection.cpp
tcp_connection.h
tcp_data_message.pb.cc
tcp_data_message.pb.h
tcp_io_device.cpp
tcp_io_device.h
test_mem.cpp
test_mem.h
test_program.cpp
test_program.h
time_buffer.h
time_core.cpp
time_core.h
time_job.cpp
time_job.h
submodules/CoreLibrary/CoreLibrary/types.h
usr_operators/types.h
usr_operators.cpp
usr_operators.h
utils.cpp
AERA/IODevices/TCP/AERA_Protobuf/utils.h
r_code/utils.h
submodules/CoreLibrary/CoreLibrary/utils.h
utils.tpl.cpp
video_screen.cpp
video_screen.h
video_screen_io_device.cpp
video_screen_io_device.h
view.cpp
view.h
view.inline.cpp
xml_parser.cpp
xml_parser.h